3D nanochannel interleaved devices for molecular manipulation are provided. In one aspect, a method of forming a device includes: forming a pattern on a substrate of alternating mandrels and spacers alongside the mandrels; selectively removing the mandrels from a front portion of the pattern forming gaps between the spacers; selectively removing the spacers from a back portion of the pattern forming gaps between the mandrels; filling i) the gaps between the spacers with a conductor to form first electrodes and ii) the gaps between the mandrels with the conductor to form second electrodes; and etching the mandrels and the spacers in a central portion of the pattern to form a channel (e.g., a nanochannel) between the first electrodes and the second electrodes, wherein the first electrodes and the second electrodes are offset from one another across the channel, i.e., interleaved. A device formed by the method is also provided.